Hi,
Were both Amber installations at the same patch level?
-Dan
On Wed, May 21, 2014 at 7:55 AM, Indrajit Deb <biky2004indra.gmail.com> wrote:
> Dear Amber users,
>
> I am facing a peculiar problem in running AMBER (Amber12 and AmberTools13).
> I have complied AMBER on 21/05/2014 in a machine having 64 bit Ubuntu 12.04
> LTS (server edition) with AMD opteron 6200 (16 core). During the NVT
> equilibration process *(tem0=300.0K)* in explicit solvent the temp. reaches
> to ~4000.0K and it stays tiil the NSLIM.
> *Output*
> ------------------------------------------------------------------------------
> NSTEP = 5000 TIME(PS) = 10.000 *TEMP(K) = 3908.32* PRESS =
> 0.0
> Etot = 90471.3668 EKtot = 89960.2013 EPtot =
> 511.1655
> BOND = 674.8848 ANGLE = 1395.6137 DIHED =
> 718.0662
> 1-4 NB = 243.6672 1-4 EEL = -394.4273 VDWAALS =
> 8058.9215
> EELEC = -11037.0200 EHBOND = 0.0000 RESTRAINT =
> 851.4594
> EAMBER (non-restraint) = -340.2939
> Ewald error estimate: 0.1491E+00
> ------------------------------------------------------------------------------
>
> Whereas when I recompiled the same AMBER on the same date in another
> machine having 64bit Ubuntu 12.04 LTS (Desktop version) with Intel Xeon
> E5-2609 (8 core), the same simulation (as mentioned above) goes fine, where
> it satisfies the *temp0*.
> *Output*
> ------------------------------------------------------------------------------
> NSTEP = 5000 TIME(PS) = 10.000 *TEMP(K) = 302.91* PRESS =
> 0.0
> Etot = -30535.4721 EKtot = 6972.1931 EPtot =
> -37507.6652
> BOND = 163.7116 ANGLE = 320.7394 DIHED =
> 466.8314
> 1-4 NB = 163.3470 1-4 EEL = -363.6741 VDWAALS =
> 4497.9322
> EELEC = -42858.9286 EHBOND = 0.0000 RESTRAINT =
> 102.3757
> EAMBER (non-restraint) = -37610.0410
> Ewald error estimate: 0.5023E-04
> ------------------------------------------------------------------------------
>
> Kindly suggest what could be the reason for this and what should be done in
> this case if I am also willing to use the first machine (having AMD
> opteron)?
>
>
> Looking forward for your reply.
>
>
> ---------------------------------------------------------------------
> Indrajit Deb
> Kolkata, India.
> Mob: +919239202278
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 21 2014 - 07:30:02 PDT
